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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agttcccaatgattgttttattcgttatgcattggattactgagagcattaccagatccaacctcttctcacaaccaatgccataatattttctttgcagGTGTTCCTTTTATACTTAAAGCAGGGAAAGCACTAAATTCAAGGAAGGCAGAAATTCGCATTCAATTCAAGGATGTTCCTGGTGATATCTACAGAT

Basic information

species Vitis vinifera
transcript Vv14s0171g00490.t01
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv14s0171g00490.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: LOC_Os04g40874.1 (Oryza sativa), 3'ss of exon 10
--------------------------------agttcccaatgattgttttattcgttatgcattggattactgagagcattaccagatccaacctcttctcacaaccaatgccataatatt--ttctttgcagGTGTTCCTTTTATACTTAAAGCAGGGAAAGCACTAAATTCAAGGAAGGCAGAAATTCGCATTCAATTCAAGGATGTTCCTGGTGATATCTACAGAT
                                 ||||   |  |       |||  || |   ||    | | ||  |  || |      | |    |  |||     ||  |  |||||||  |    ||||||||||||||| || |||||||| || ||||||||||  |||||||| |||||| | ||  | || ||||| |||||||||||||| ||||  | ||
gtatgtctctcatcagtatatatacacattagggttctggagaaggacaacattgattttcgttttcccttcagattgtctttcagtggaccataattcttcatt-ttaactctgtaatattcatatcctgcagGTGTTCCTTTCATTCTTAAAGCTGGTAAAGCACTAAGCTCAAGGAAAGCAGAAGTCCGTGTGCAGTTCAAAGATGTTCCTGGTGACATCTTTAAAT

upper sequence: Vv14s0171g00490.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GRMZM2G130230_T03 (Zea mays), 3'ss of exon 11
-----------------------------------------------------agttcccaatgattgttttattcgttatgcattggattactgagagcattaccagatccaacctcttctcacaaccaatgccataatatt--ttctttgcagGTGTTCCTTTTATACTTAAAGCAGGGAAAGCACTAAATTCAAGGAAGGCAGAAATTCGCATTCAATTCAAGGATGTTCCTGGTGATATCTACAGAT
                                                        |   |||  ||| | | |   || | ||||  ||         |   |||| |       |  | ||   | |||     |||||||  | |||||||||||||||||| || |||||||| || |||||| | | ||||| ||| |||||| ||||  | |||||||||||||| |||||||| || |  ||| 
gtatatcttcacccacatgacagtatctgtacatattgtagttgaaatggatataattgaaatacttgctctctgtttttttcattcaatgtgccttttctcaaccataatatctttactttctgtatcaaccttctaatattcatgctttgcagGTGTTCCTTTCATTCTTAAAGCTGGTAAAGCATTGAGTTCAAAGAAAGCAGAAGTTCGGGTGCAATTCAAGGATGTCCCTGGTGACATTTTTAGAA

upper sequence: Vv14s0171g00490.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA16G06850.3 (Glycine max), 3'ss of exon 11
----------------------------------------agttcccaatgattgttttattcgttatgcattggattactgagagcattac----cagatccaacctcttctcacaaccaatgccata-atattttctttg-cagGTGTTCCTTTTATACTTAAAGCAGGGAAAGCACTAAATTCAAGGAAGGCAGAAATTCGCATTCAATTCAAGGATGTTCCTGGTGATATCTACAGAT
                                        | | |  ||   |  ||| |||  ||  |      | |   || |  |        || || ||  ||  |  |  ||  ||    ||| ||||||| | |  ||||||||||||| ||||| ||||||||||| ||||||||||| || |||||||| ||  |  |||||||||||||||| ||||||||||| | ||  |
gtcagatgaaatgttgaacatttccttcctaaaagaaataaatactgaagcttcctttaatttctttggtgcaaaaattaggaaaatacagtagttcatattcattctggtgcctaaaagaagtatatatatattttttgtatcagGTGTTCCTTTCATACTAAAAGCAGGGAAGGCACTAAATTCTAGAAAGGCAGAGATAAGGGTTCAATTCAAGGATGTCCCTGGTGATATTTTCAAGT

upper sequence: Vv14s0171g00490.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA19G24250.1 (Glycine max), 3'ss of exon 11
---------------------------------------agttcccaatgattgttttattcgttatgcattggattactgagagcattac-cagatccaacctcttctcacaaccaatgccataatattttctttg-cagGTGTTCCTTTTATACTTAAAGCAGGGAAAGCACTAAATTCAAGGAAGGCAGAAATTCGCATTCAATTCAAGGATGTTCCTGGTGATATCTACAGAT
                                          | |    | ||  |||| |   | ||      |  | |  ||  || |   || ||  |    ||||     | |||   ||  | ||||   |  |||||||||| || ||||| ||||||||||| ||||||||||| || |||||||| ||  |  |||||||||||||||| ||||||||||| | ||  |
gtcagatgaaatgttaagcatttccttcctaaaagaaatgaatactggagcttcctttaatttctttggtgcaaaaaattaggaaaataaagtagttcatattcattctggtgcctaatagaattttttttttggtatcagGTGTTCCGTTCATACTAAAAGCAGGGAAGGCACTAAATTCTAGAAAGGCAGAGATCAGGGTTCAATTCAAGGATGTCCCTGGTGATATTTTCAAGT

upper sequence: Vv14s0171g00490.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA19G22690.1 (Glycine max), 3'ss of exon 11
agttcccaatgattgttttattcgttatgcattggattactgagagcattaccagatccaacctcttctcacaaccaatgccataatattttctttgc------agGTGTTCCTTTTATACTTAAAGCAGGGAAAGCACTAAATTCAAGGAAGGCAGAAATTCGCATTCAATTCAAGGATGTTCCTGGTGATATCTACAGAT
   |       ||| |||| |   ||||||  |  ||| ||| |    | | ||  |  ||  |    ||  ||| | |  || |  |  | ||||        |||||||||||| ||||| || || ||||| ||  ||||||| || |||||||| || ||  |||||||||||||||||||||||||||| |  |  |
---ttgtgtgtattattttgtattttatgctatatatttctgtgcatttgatcaatt--aaattgcaatcgaaac-attttcacaccagctcctttctgatgttagGTGTTCCTTTCATACTAAAGGCTGGGAAGGCCTTAAATTCGAGAAAGGCAGACATACGGGTTCAATTCAAGGATGTTCCTGGTGATATTTTTAAGT

upper sequence: Vv14s0171g00490.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: AT5G40760.1 (Arabidopsis thaliana), 3'ss of exon 11
agttcccaatgattgttttattcgttatgcattggattactgagagcattaccaga-tccaacctcttctcacaaccaatgccataat-----attttctttgcagGTGTTCCTTTTATACTTAAAGCAGGGAAAGCACTAAATTCAAGGAAGGCAGAAATTCGCATTCAATTCAAGGATGTTCCTGGTGATATCTACAGAT
        |||||  |      | | |  | || | |||  |   |    |||| | ||| || | ||  ||    || |   |   |     || |   || |||||||||| |||||| | || || || |||||  | ||||||||||||||||||||||||||||||||||||||||| || || || || | |||||
------acatgatcatagatagcatcaatcttttggttaaagcatgtggaaccaaaatccgacatgtttgcatgcacattctaacggtcctggatatatctttcagGTGTTCCATTTATATTAAAGGCCGGAAAAGCGTTGAATTCAAGGAAGGCAGAAATTCGCATTCAATTCAAGGATGTCCCAGGCGACATATTCAGAT

upper sequence: Vv14s0171g00490.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: AT3G27300.2 (Arabidopsis thaliana), 3'ss of exon 12
-------------agttcccaatgattgttttattcgttatgcattggatta--ctgagagcattaccagatccaacctcttctca-------caaccaatgccata-atatt----ttctttgcagGTGTTCCTTTTATACTTAAAGCAGGGAAAGCACTAAATTCAAGGAAGGCAGAAATTCGCATTCAATTCAAGGATGTTCCTGGTGATATCTACAGAT
                ||||  | | | ||    |  | ||    | ||| |   |  || ||| |   |    || | ||| | |            | |  | |   ||||    |   |  ||||||||||||||||||| || || || || ||| | | ||||| ||||||||| ||||||||||| || || ||||||||||| || || | || ||
gtactgtgtgcatgtgtccccttcactcttcatcttttcattttctagatcaagtttggaacatcatgtgccaaaatccctttttagttgtagtggttagtaacttgtgtattgatgtatctctcagGTGTTCCTTTTATACTGAAGGCCGGAAAGGCAATGAGTTCAAAGAAGGCAGATATTCGCATTCAGTTTAAAGATGTTCCTGGCGACATATTCAAAT

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|30299156|gb|CB975950.1|CB975950
EST:     CCCAACTTTTGCATCTATGATTCTGCGTATACACAATGAAAGATGGGAAG                         GTGTTCCTTTTATACTTAAAGCAGGGAAAGCACTNANTTCAAGGAAGGCAG
genomic: CCCAACTTTTGCATCTATGATTCTGCGTATACACAATGAAAGATGGGAAGgtgtgagaat ... ttctttgcagGTGTTCCTTTTATACTTAAAGCAGGGAAAGCACTAAATTCAAGGAAGGCAG
EST: gi|351015046|gb|FQ444335.1|FQ444335
EST:     CCCAACTTTTGCATCTATGATTCTGCGTATACACAATGAAAGATGGGAAG                         GTGTTCCTTTTATACTTAAAGCAGGGAAAGCACTAAATTCAAGGAAGGCAG
genomic: CCCAACTTTTGCATCTATGATTCTGCGTATACACAATGAAAGATGGGAAGgtgtgagaat ... ttctttgcagGTGTTCCTTTTATACTTAAAGCAGGGAAAGCACTAAATTCAAGGAAGGCAG
EST: gi|110365367|gb|EC928242.1|EC928242
EST:     CCCAACTTTTGCATCTATGATTCTGCGTATACACAATGAAAGATGGGAAG                         GTGTTCCTTTTATACTTAAAGCAGGGAAAGCACTAAATTCAAGGAAGGCAG
genomic: CCCAACTTTTGCATCTATGATTCTGCGTATACACAATGAAAGATGGGAAGgtgtgagaat ... ttctttgcagGTGTTCCTTTTATACTTAAAGCAGGGAAAGCACTAAATTCAAGGAAGGCAG
EST: gi|33405782|gb|CF211409.1|CF211409
EST:     CCCAACTTTTGCATCTATGATTCTGCGTATACACAATGAAAGATGGGAAG                         GTGTTCCTTTTATACTTAAAGCAGGGAAAGCACTAAATTCAAGGAAGGCAG
genomic: CCCAACTTTTGCATCTATGATTCTGCGTATACACAATGAAAGATGGGAAGgtgtgagaat ... ttctttgcagGTGTTCCTTTTATACTTAAAGCAGGGAAAGCACTAAATTCAAGGAAGGCAG
EST: gi|110361886|gb|EC925389.1|EC925389
EST:     CCCAACTTTTGCATCTATGATTCTGCGTATACACAATGAAAGATGGGAAG                         GTGTTCCTTTTATACTTAAAGCAGGGAAAGCACTAAATTCAAGGAAGGCAG
genomic: CCCAACTTTTGCATCTATGATTCTGCGTATACACAATGAAAGATGGGAAGgtgtgagaat ... ttctttgcagGTGTTCCTTTTATACTTAAAGCAGGGAAAGCACTAAATTCAAGGAAGGCAG
EST: gi|294967142|gb|GW840017.1|GW840017
EST:     CCCAACTTTTGCATCTATGATTCTGCGTATACACAATGAAAGATGGGAAG                         GTGTTCCTTTTATACTTAAAGCAGGGAAAGCACTAAATTCAAGGAAGGCAG
genomic: CCCAACTTTTGCATCTATGATTCTGCGTATACACAATGAAAGATGGGAAGgtgtgagaat ... ttctttgcagGTGTTCCTTTTATACTTAAAGCAGGGAAAGCACTAAATTCAAGGAAGGCAG
EST: gi|110696408|gb|EE072500.1|EE072500
EST:     CCCAACTTTTGCATCTATGATTCTGCGTATACACAATGAAAGATGGGAAG                         GTGTTCCTTTTATACTTAAAGCAGGGAAAGCACTAAATTCAAGGAAGGCAG
genomic: CCCAACTTTTGCATCTATGATTCTGCGTATACACAATGAAAGATGGGAAGgtgtgagaat ... ttctttgcagGTGTTCCTTTTATACTTAAAGCAGGGAAAGCACTAAATTCAAGGAAGGCAG
EST: gi|56409520|gb|CX017772.1|CX017772
EST:     CCCAACTTTTGCATCTATGATTCTGCGTATACACAATGAAAGATGGGAAG                         GTGTTCCTTTTATACTTAAAGCAGGGAAAGCACTAAATTCAAGGAAGGCAG
genomic: CCCAACTTTTGCATCTATGATTCTGCGTATACACAATGAAAGATGGGAAGgtgtgagaat ... ttctttgcagGTGTTCCTTTTATACTTAAAGCAGGGAAAGCACTAAATTCAAGGAAGGCAG
EST: gi|110416304|gb|EC982275.1|EC982275
EST:     CCCAACTTTTGCATCTATGATTCTGCGTATACACAATGAAAGATGGGAAG                         GTGTTCCTTTTATACTTAAAGCAGGGAAAGCACTAAATTCAAGGAAGGCAG
genomic: CCCAACTTTTGCATCTATGATTCTGCGTATACACAATGAAAGATGGGAAGgtgtgagaat ... ttctttgcagGTGTTCCTTTTATACTTAAAGCAGGGAAAGCACTAAATTCAAGGAAGGCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcattaccagatccaacctcttctcacaaccaatgccataatattttctttgcagGTGTTCCTTTTATACTTAAAGCAGGGAAAGCACTAAATTCAAGGAAGGCAGAAATTCGCATTCAATTCAAGGATGTTCCTGGTGATATCTACAGAT
                    ttctcac  putative branch site (score: 2)
                                         tattttcttt  putative PPT
                                     ataatattttcttt  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agttcccaatgattgttttattcgttatgcattggattactgagagcattaccagatccaacctcttctcacaaccaatgccataatattttctttgcagGTGTTCCTTTTATACTTAAAGCAGGGAAAGCACTAAATTCAAGGAAGGCAGAAATTCGCATTCAATTCAAGGATGTTCCTGGTGATATCTACAGAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG
- - cccaatg
- - - - - - - - - - - - - -tgcattg
- - - - - - - - - - - - - - - - - - - - - - - cattacc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - acaacca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -atgccat